Anki rarely gets new features. This must have been discussed before. I’d search the old forum at anki.tenderapp.com and the anki subreddit. Maybe some combination of workarounds or add-ons help?
An idea for a manual workaround:
You could give all your notes in your external file a tag that doesn’t change like “from_genanki” an another like “updated_2020-11-12”. Whenever you change any note in the source you change the latter tag in the source for all notes to the current date etc.
Then you import into Anki. For all notes that you import the tag will be updated. For notes that you have deleted in the source the tag will not be updated so deleted notes won’t have this updated tags. You should be able to find them with a search like tag:from_genanki -tag:updated_2020-11-12 and then you can delete them?